When you go up at the junction, have a Charge Shot ready to use as you will quickly find multiple small groups of enemies. Slippy will then force out a couple of extra groups for you to take care of. However, Slippy will find too many to handle the third time around, so lock on and fire a Smart Bomb to keep him safe. Take out the turrets up ahead and then Falco will tell you to take the next group down with one shot. You can simply use a couple of Charge Shots to rack up a few extra hits. There will be a few more turrets to take out up ahead before Slippy, Falco, and Peppy fly in a triangle formation up ahead. You can choose to form a diamond formation with them by using the boost to catch up with them in order to get a "1UP", or you can lag behind and use Charge Shots to shoot at the enemies trying to hit them. R0B 64 will confirm your location after that and send supplies. Take out the 3 groups of enemies with Charge Shots to really rack up some hits before emerging out of the Melee. Slippy will then notice a different kind of enemy up ahead and alert the team. Fox will tell the team to enter all-range mode and then the fight with the Shogun Warriors will begin. They are annoyingly quick, so be careful to not accidentally shoot your wingmates. Once you take them out, Combat Robot Shogun will appear and attempt to take out the Star Fox Team. He is even faster than the Shogun Warriors and he has a shield that can defend against your laser fire for a short time. Once he drops below half health, the shield will break off, thus allowing you to hit him more easily. Once you defeat Combat Robot Shogun, Fox will tell the team that they're headed for Aquas.

General Pepper will ask the Star Fox Team to take out the enemy's bio-weapon in Aquas. Upon this, Fox will order the deployment of the Blue Marine. This is the only mission where Fox will be alone without Peppy, Slippy, and Falco there to help him directly. The Blue Marine is special in that it doesn't use bombs, but has infinite torpedoes instead. Those torpedoes will be your main weapons here as the Blue Marine's lasers are rather weak when compared to the Arwing and even the Landmaster. The level is fairly straightforward with hordes of enemies to take out. Using torpedoes often can not only take out many enemies, but it also helps you to see better in the dark, murky waters. During the level, it's revealed that Slippy is the one who made the Blue Marine and suggested that the team bring it along with them, just in case. Being the air lover that he is, Falco will continually bash the Blue Marine and say that it'll never pull through. Keep on going, and you'll see that it will pull through. Once you reach the Checkpoint, you are near the end of the level.